High-resolution HLA-typing by next-generation sequencing of randomly fragmented target DNA

Abstract

PCR- or probe-based targeted capturing enables the enrichment of specific genomic loci prior to Next-Generation Sequencing (NGS). Here, we describe a probe-based protocol, which allows for high-resolution HLA typing of DNA samples by NGS. We also describe existing software tools that can be used for the subsequent HLA data analysis. Key prerequisites that warrant an accurate HLA calling are specific mappings of the sequencing reads, phasing of the mapped reads, and the possibility to perform a manual inspection/curation of the read mapping.